The present invention is directed to methods for synthesizing oligonucleotides and analogs thereof. In one aspect of the invention the methods combine oxidation and capping into a single step to improve the efficiency of synthesis. The overall synthesis preferably is completed in less time with a reduction in bulk reagents required. More specific objectives and advantages of the invention will hereinafter be made clear or become apparent to those skilled in the art during the course of explanation of preferred embodiments of the invention.
Modified oligonucleotides are of great value in molecular biological research and in applications such as anti-viral therapy. Modified oligonucleotides which can block RNA translation, and are nuclease resistant, are useful as antisense reagents. In addition to oligonucleotides that have phosphodiester internucleotide linkages, sulfurized oligonucleotides which contain, for example, phosphorothioate linkages are also of interest in these areas. Because of their chirality (Rp and Sp) phosphorothioate containing oligonucleotides are useful in determining stereochemical pathways of certain enzymes which recognize nucleic acids.
It is well known that most of the bodily states in multicellular organisms, including most disease states, are effected by proteins. Such proteins, either acting directly or through their enzymatic or other function, contribute in major proportion to many diseases and regulatory functions in animals and humans. For disease states, classical therapeutics has generally focused upon interactions with such proteins in efforts to moderate their disease-causing or disease-potentiating functions. In newer therapeutic approaches, modulation of the actual production of such proteins is desired. By interfering with the production of proteins, the maximum therapeutic effect may be obtained with minimal side effects. It is therefore a general object of such therapeutic approaches to interfere with or otherwise modulate gene expression, which would lead to undesired protein formation.
One method for inhibiting specific gene expression is with the use of oligonucleotides, especially oligonucleotides which are complementary to a specific target messenger RNA (mRNA) sequence. Several oligonucleotides are currently undergoing clinical trials for such use. Phosphorothioate oligonucleotides are presently being used as such antisense agents in human clinical trials for various disease states, including use as antiviral agents.
Transcription factors interact with double-stranded DNA during regulation of transcription. Oligonucleotides can serve as competitive inhibitors of transcription factors to modulate their action. Several recent reports describe such interactions (see Bielinska, A., et. al., Science, 1990, 250, 997-1000; and Wu, H., et. al., Gene, 1990, 89, 203-209).
In addition to such use as both indirect and direct regulators of proteins, oligonucleotides and their analogs also have found use in diagnostic tests. Such diagnostic tests can be performed using biological fluids, tissues, intact cells or isolated cellular components. As with gene expression inhibition, diagnostic applications utilize the ability of oligonucleotides and their analogs to hybridize with a complementary strand of nucleic acid. Hybridization is the sequence specific hydrogen bonding of oligomeric compounds via Watson-Crick and/or Hoogsteen base pairs to RNA or DNA. The bases of such base pairs are said to be complementary to one another.
Oligonucleotides and their analogs are also widely used as research reagents. They are useful for understanding the function of many other biological molecules as well as in the preparation of other biological molecules. For example, the use of oligonucleotides and their analogs as primers in PCR reactions has given rise to an expanding commercial industry. PCR has become a mainstay of commercial and research laboratories, and applications of PCR have multiplied. For example, PCR technology now finds use in the fields of forensics, paleontology, evolutionary studies and genetic counseling. Commercialization has led to the development of kits which assist non-molecular biology-trained personnel in applying PCR. Oligonucleotides and their analogs, both natural and synthetic, are employed as primers in such PCR technology.
Oligonucleotides and their analogs are also used in other laboratory procedures. Several of these uses are described in common laboratory manuals such as Molecular Cloning, A Laboratory Manual, Second Ed., J. Sambrook, et al., Eds., Cold Spring Harbor Laboratory Press, 1989; and Current Protocols In Molecular Biology, F. M. Ausubel, et al., Eds., Current Publications, 1993. Such uses include as synthetic oligonucleotide probes, in screening expression libraries with antibodies and oligomeric compounds, DNA sequencing, in vitro amplification of DNA by the polymerase chain reaction, and in site-directed mutagenesis of cloned DNA. See Book 2 of Molecular Cloning, A Laboratory Manual, supra. See also xe2x80x9cDNA-protein interactions and The Polymerase Chain Reactionxe2x80x9d in Vol. 2 of Current Protocols In Molecular Biology, supra.
Oligonucleotides and their analogs can be synthesized to have customized properties that can be tailored for desired uses. Thus a number of chemical modifications have been introduced into oligomers to increase their usefulness in diagnostics, as research reagents and as therapeutic entities. Such modifications include those designed to increase binding to a target strand (i.e. increase their melting temperatures, Tm), to assist in identification of the oligonucleotide or an oligonucleotide-target complex, to increase cell penetration, to stabilize against nucleases and other enzymes that degrade or interfere with the structure or activity of the oligonucleotides and their analogs, to provide a mode of disruption (terminating event) once sequence-specifically bound to a target, and to improve the pharmacokinetic properties of the oligonucleotide.
The synthesis of oligonucleotides has classically involved obtaining a desired product on a small scale. The synthesis of oligonucleotides has more recently evolved to the point that routine syntheses are being performed on kilogram scale. Moving forward the next step is the synthesis of oligonucleotides and analogs on ton scale to supply large quantities to meet demands for ongoing pharmaceutical sales and clinical trials. The evolution of oligonucleotide synthetic techniques toward larger scale is requiring a reevaluation of each aspect of the synthetic process. There is an ongoing need in the art of oligomer synthesis to improve the efficiency of synthesis.
The chemical literature discloses numerous protocols for coupling nucleosides through phosphorous-containing covalent linkages to produce oligonucleotides of defined sequence. One of the most routinely used protocols is the phosphoramidite protocol (see, e.g, Advances in the Synthesis of Oligonucleotides by the Phosphoramidite Approach, Beaucage, S. L.; Iyer, R. P., Tetrahedron, 1992, 48, 2223-2311 and references cited therein; and The synthesis of Modified Oligonucleotides by the Phosphoramidite Approach and their applications, Beaucage, S. L.; Iyer, R. P., Tetrahedron, 1993, 49, 6123-6194 and references cited therein), wherein a nucleoside or oligonucleotide having a free hydroxyl group is reacted with a protected phosphoramidite monomer in the presence of a weak acid to form a phosphite-linked structure. Oxidation of the phosphite linkage with a suitable reagent effects conversion of a PIII internucleoside linkage to a PV internucleoside linkage. For the purpose of this application, such reagents include oxygen transfer reagents and sulfur transfer reagents. Subsequent hydrolysis of the cyanoethyl group yields the desired phosphodiester or phosphorothioate linkage.
Phosphoramidites are commercially available from a variety of commercial sources (included are: Glen Research, Sterling, Va.; Amersham Pharmacia Biotech Inc., Piscataway, N.J.; Cruachem Inc., Aston, Pa.; Chemgenes Corporation, Waltham, Mass.; Proligo LLC, Boulder, Colo.; PE Biosystems, Foster City Calif.; Beckman Coulter Inc., Fullerton, Calif.).
An efficient sulfur transfer reagent is important to the success of obtaining high quality phosphorothioate product with a low percentage of phosphate linkages. A number of sulfur transfer reagents have been reported, including Beaucage reagent, 3-ethoxy-1,2,4-dithiozloine-5-one (EDITH), 1,2,4-dithiozoline-3,5-dione, 3-methyl-ethoxy-1,2,4-dithiozloine-5-one (MEDITH), phenylacetyl disulfide (PADS), tetraethylthiuram disulfide (TETD) and others. The cost of sulfur transfer reagents and their efficiency has to be taken into account when performing large-scale manufacturing. Beaucage reagent is expensive (about $5.00 per gram) and is being replaced by other cheaper reagents like PADS. PADS was first introduced by van Boom but did not show adequate sulfur transfer efficiency under the original conditions, which did not use a base during the sulfurization step (Roclen et al., Recl. Trav. Chim. Pays-Bas, 1991, 110, 325-331).
The use of elemental sulfur in olignucleotide synthesis presents problems and is not suitable for automation because of sulfur""s insolubility in most organic solvents. Furthermore, carbon disulfide, a preferred source of sulfur, has undesirable volatility and an undesirably low flash point. Unwanted side products are often observed with the use of dibenzoyl tetrasulfide. Beaucage reagent, while a relatively efficient sulfurization reagent, is difficult to synthesize and not particularly stable. Furthermore, use of Beaucage reagent forms a secondary reaction product which is a potent oxidizing agent. (R. P. Iyer et al., J. Am. Chem. Soc. 112, pp. 1253-1254 (1990); R. P. Iyer et al., J. Org. Chem. 55, 4693-4699 (1990)). This can further lead to unwanted side products which can be difficult to separate from the desired reaction product. Tetraethylthiuram disulfide while relatively inexpensive and stable, has a sulfurization reaction rate which can be undesirable slow.
A method of preparing phosphorothioate oligonucleotides using tetraethylthiuram disulfide is disclosed in U.S. Pat. No. 5,166,387. Although the use of tetraethylthiuram disulfide as a sulfur transfer reagent has been described since 1992, it has not been used for commercial scale production of phosphorothioate oligonucleotides. Beaucage reagent and phenylacetyl disulfide (PADS) are the only reagents that have been used commercially with good results. Our experiments with tetraethylthiuram disulfide indicate that there is a significant amount of side product formation (see Example 8) along with the desired phosphorothioate product. Although we do not wish to be bound by theory it is believed that tetraethylthiuram disulfide is an overly stable sulfur transfer reagent that is difficult to dissociate after reaction with the PIII species.
Thus, there remains a need for improved methods and reagents for preparing oligomeric compounds. The present invention is directed to these, as well as other, important ends.
The present invention provides methods of preparing oligomeric compounds having at least one moiety of formula: 
wherein:
X2 is O or S;
X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, C1-C10 straight or branched chain alkyl, CH3(CH2)nnxe2x80x94Oxe2x80x94, R2R3Nxe2x80x94 or a group remaining from coupling a chiral auxiliary;.
nn is from 0 to 10;
Pg is CH3, xe2x80x94CH2CH2CN, xe2x80x94C(CH3) (CH3)xe2x80x94CCl3, xe2x80x94CH2-CCl3, xe2x80x94CH2CHxe2x95x90CH2, CH2CH2SiCH3, 2-yl-ethyl phenylsulfonate, xcex4-cyano-butenyl, cyano p-xylyl, diphenylsilylethyl, 4-nitro-2-yl-ethylbenzene, 2-yl-ethyl-methyl sulfonate, methyl-N-trifluoroacetyl ethyl, acetoxy phenoxy ethyl, or a blocking group;
each R2 and R3 is, independently, hydrogen, C1-C10 alkyl, cycloalkyl or aryl;
or optionally, R2 and R3, together with the nitrogen atom to which they are attached form a cyclic moiety that may include an additional heteroatom selected from O, S and N;
each Bx is, independently, a heterocyclic base moiety; and
each R1 is, independently, H, a blocked hydroxyl group, or a sugar substituent group; comprising the steps of:
(a) providing a 5xe2x80x2-O-protected compound of the formula: 
wherein:
T1 is a hydroxyl protecting group; and
T2 is a covalent attachment to a support media, a nucleoside bound to a support media, a nucleotide, an oligonucleoside or an oligonucleotide;
(b) treating said 5xe2x80x2-O-protected compound with a deprotecting reagent for a time and under conditions effective to form a 5xe2x80x2-O-deprotected compound;
(c) coupling said 5xe2x80x2-O-deprotected compound with an activated phosphorus composition of the formula: 
wherein:
T3 is a hydroxyl protecting group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
R4 is N(L1)L2;
each L1 and L2 is, independently, C1-6 straight or branched alkyl, or a C5-7 cyclic aliphatic ring system;
or L1 and L2 are joined together to form a 4- to 13-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S; and
R5 is X1;
or R4 and R5 together with the phosphorus atom to which R4 and R5 are attached form a chiral auxiliary;
for a time and under conditions effective to form an extended compound having the formula: 
(d) treating said extended compound with a mixture comprising an oxidizing reagent and a capping reagent for a time and under conditions effective to form said oligomeric compound.
The methods can include further treatment of the oligomeric compound with a reagent for a time and under conditions effective to remove the blocking groups, thereby forming a deblocked oligomeric compound. This reagent can also be effective to cleave the oligomeric compound from the support media. One such reagent is aqueous ammonium hydroxide. Alternatively, the deblocking can be effected with one reagent, and a further reagent can effect cleavage from the support media. Also included is treatment with a deprotecting reagent for a time and under conditions effective to deprotect the T3 hydroxyl protecting group.
In one embodiment of the invention, the mixture comprises from 0.02M to 0.2M oxidizing reagent with a preferred range is from 0.1M to 0.2M.
The oxidizing reagent can be one that transfers an oxygen atom. Effective oxidizing reagents for oxygen transfer are iodine, m-chloroperbenzoic acid, iodobenzene diacetate, tetra-n-butylammonium periodate, tert-butyl hydroperoxide, di-tert-butyl hydroperoxide, cumene hydroperoxide, hydrogen peroxide; bis-trimethylsilyl peroxide; dinitrogen tetroxide, oxone, molecular oxygen, (1S)-(+)-(10-camphorsulfonyl)oxaziridine or a peracid with iodine, m-chloroperbenzoic acid, iodobenzene diacetate, tert-butyl hydroperoxide, di-tert-butyl hydroperoxide, hydrogen peroxide; oxone, molecular oxygen or a peracid being preferred.
The oxidizing reagent can also be one that transfers a sulfur atom. Effective oxidizing reagents for sulfur transfer are 3-amino-1,2,4-dithiazole-5-thione; 3-ethoxy-1,2,4-dithiazoline-5-one; 1,2,4-dithiazolidine-3,5-dione; 3-methyl-1,2,4-dithiazolin-5-one; or dimethylthiuram disulfide with dimethylthiuram disulfide being preferred.
In one embodiment, the capping reagent is prepared by mixing equal volumes of two components prior to the capping step. The first component is a mixture of an acylating agent such as N-methylimidazole or 4-dimethylaminopyridine and a base such as pyridine or 2,6-lutidine in acetonitrile or tetrahydrofuran. The second component is a solution of an acid anhydride such as acetic anhydride, chloroacetic anhydride, t-butylphenoxyacetic anhydride in acetonitrile or tetrahydrofuran.
One preferred capping reagent comprises about equal volumes of a first component containing from 5% to about 25% N-methylimidazole, from about 20% to about 50% pyridine and from about 20% to about 50% acetonitrile, added to a second component containing from about 20% to about 50% acetic anhydride in acetonitrile.
Another preferred capping reagent comprises about equal volumes of a first component containing about 5% to about 25% 4-dimethylaminopyridine, from about 20% to about 50% 2,6-lutidine in acetonitrile, added to a second component containing from about 20% to about 50% acetic anhydride in acetonitrile.
The mixture of oxidizing reagent and capping reagent can comprise, for example, dimethylthiuram disulfide, acetic anhydride, acetonitrile, N-methyl imidazole, or pyridine. A preferred mixture comprises from about 0.05M to 0.2M dimethylthiuram disulfide, about 10% acetic anhydride, about 10% N-methyl imidazole and about 15% pyridine in a suitable solvent. Suitable solvents include acetonitrile, toluene, ethyl acetate, tetrahydrofuran, dichloromethane, dichloroethane, dioxane, dimethylacetamide and dimethylformamide.
In another embodiment of the invention the coupling of the 5xe2x80x2-O-deprotected compound with the activated phosphorus composition is performed in the presence of an activating agent that renders the phosphorous atom more susceptible to nucleophilic attack. Preferred activating agents include 1-H-tetrazole and 4,5-dicyanoimidazole.
Exemplary cyclic moieties according to the invention include morpholino or phthalimido moieties.
Each L1 and L2 can be, independently, C1-6 alkyl with isopropyl being a preferred alkyl group for L1 and L2. L1 and L2 can also be joined together to form a heterocyclic ring system including the nitrogen atom to which said L1 and L2 are attached, the ring system optionally includes at least one additional heteroatom selected from O, N and S. A preferred heterocyclic ring system is morpholino.
Representative substituent groups according to the invention include, C1-C20 alkyl, C2-C20 alkenyl, C2-C20 alkynyl, C5-C20 aryl, O-alkyl, O-alkenyl, O-alkynyl, O-aryl, O-aralkyl, O-alkylamino, O-alkylaminoalkyl (O-alkyl-N(H)alkyl), O-alkylaminodialkyl (O-alkyl-N-(alkyl),2), O-alkylalkoxy (O-alkyl-O-alkyl), O-alkyl-(N-imidazole), thiol, S-alkyl, S-alkenyl, S-alkynyl, NH-alkyl, NH-alkenyl, NH-alkynyl, N-dialkyl, S-aryl, NH-aryl, S-aralkyl, NH-aralkyl, N-phthalimido, halogen keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, N-imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, heterocycle, carbocycle, polyamine, polyamide, polyalkylene glycol, or polyether;
Alternatively, one or more substituent groups has one of formula I or II: 
wherein:
Z0 is O, S or NH;
J is a single bond, O or C(xe2x95x90O);
E is C1-C10 alkyl, N(R1) (R2), N(R1) (R5), Nxe2x95x90C(R1) (R2), Nxe2x95x90C(R1) (R5) or has one of formula III or IV; 
each R6, R7, R8, R9 and R10 is, independently, hydrogen, C(O)R11, substituted or unsubstituted C2-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl, substituted or unsubstituted C2-C10 alkynyl, alkylsulfonyl, arylsulfonyl, a chemical functional group or a conjugate group, wherein the substituent groups are selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl;
or optionally, R7 and R8, together form a phthalimido moiety with the nitrogen atom to which they are attached;
or optionally, R9 and R10, together form a phthalimido moiety with the nitrogen atom to which they are attached;
each R11 is, independently, substituted or unsubstituted C1-C10 alkyl, trifluoromethyl, cyanoethyloxy, methoxy, ethoxy, t-butoxy, allyloxy, 9-fluorenylmethoxy, 2-(trimethylsilyl)-ethoxy, 2,2,2-trichloroethoxy, benzyloxy, butyryl, isobutyryl, phenyl or aryl;
R5 is T-L,
T is a bond or a linking moiety;
L is a chemical functional group, a conjugate group or a support media;
each R1 and R2 is, independently, H, a nitrogen protecting group, substituted or unsubstituted C1-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl, substituted or unsubstituted C2-C10 alkynyl, wherein said substitution is OR3, SR3, NH3+, N(R3) (R4), guanidino or acyl where said acyl is an acid amide or an ester;
or R1 and R2, together, are a nitrogen protecting group or are joined in a ring structure that optionally includes an additional heteroatom selected from N and O;
or R1, T and L, together, are a chemical functional group;
each R3 and R4 is, independently, H, C1-C10 alkyl, a nitrogen protecting group, or R3 and R4, together, are a nitrogen protecting group;
or R3 and R4 are joined in a ring structure that optionally includes an additional heteroatom selected from N and O;
Z4 is OX, SX, or N(X)2;
each X is, independently, H, C1-C8 alkyl, C1-C8 haloalkyl, C(xe2x95x90NH)N(H)R5, C(xe2x95x90O)N(H)R5 or OC(xe2x95x90O)N(H)R5;
R5 is H or C1-C8 alkyl;
Z1, Z2 and Z3 comprise a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2 hetero atoms wherein said hetero atoms are selected from oxygen, nitrogen and sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;
Z5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R1) (R2) OR1, halo, SR1 or CN;
each q1 is, independently, an integer from 1 to 10;
each q2 is, independently, 0 or 1;
q3 is 0 or an integer from 1 to 10;
q4 is an integer from 1 to 10;
q5 is from 0, 1 or 2; and provided that when q3 is 0, q4 is greater than 1.
In one embodiment of the present invention X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, xe2x80x94CH3, CH3xe2x80x94Oxe2x80x94, morpholino or xe2x80x94NR2R3 where each R2 and R3 is, independently, hydrogen or C1-C10 alkyl. Where Pg is CH2CH2CN, diphenylsilylethyl, xcex4-cyanobutenyl, cyano p-xylyl, methyl-N-trifluoroacetyl ethyl or acetoxy phenoxy ethyl.
Representative heterocyclic bases include adenine, N6-benzoyladenine, cytosine, N4-benzoylcytosine, 5-methylcytosine, N4-benzoyl-5-methylcytosine, thymine, uracil, guanine, N2-isobutyrylguanine and 2-aminoadenine, as well as protected (or xe2x80x9cblockedxe2x80x9d) forms thereof.
In certain embodiments of the present invention, the support media bound nucleoside, nucleotide, oligonucleoside or oligonucleotide is blocked at reactive sites. In one embodiment the blocking groups are acid stable. In another embodiment the blocking groups are base labile.
Deprotecting reagents can be acidic, neutral or basic. Preferred deprotecting reagents are dichloroacetic acid, trichloroacetic acid, zinc bromide, AlCl3, TiCl4, (Et)AlCl, (I-Bu)2AlCl, ceric ammonium nitrate, 1,1,1,3,3,3-hexafluoro-2-propanol, and diethyloxomalonate. A particularly preferred deprotecting reagent is 2-5% dichloroacetic acid in dichloromethane or dichloroethane. In a further embodiment the deprotecting reagent is a fluoride moiety where a preferred fluoride moiety is BF3-etherate.
The oligomeric compounds of the invention typically comprises from 5 to about 50 nucleosides, with from 8 to about 30 nucleosides being preferred and from 15 to about 25 nucleosides being more preferred.
The present invention also provides methods for the preparation of oligomeric compounds having at least one moiety of formula: 
wherein:
X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, C1-C10 straight or branched chain alkyl, CH3(CH2)nnxe2x80x94Oxe2x80x94, R2R3Nxe2x80x94 or a group remaining from coupling a chiral auxiliary;
nn is from 0 to 10;
Pg is CH3, xe2x80x94CH2CH2CN, xe2x80x94C(CH3) (CH3)xe2x80x94CCl3, xe2x80x94CH2xe2x80x94CCl3, xe2x80x94CH2CHxe2x95x90CH2, CH2CH2SiCH3, 2-yl-ethyl phenylsulfonate, xcex4-cyanobutenyl, cyano p-xylyl, diphenylsilylethyl, 4-nitro-2-yl-ethylbenzene, 2-yl-ethyl-methyl sulfonate, methyl-N-trifluoroacetyl ethyl, acetoxy phenoxy ethyl, or a blocking group;
each R2 and R3 is, independently, hydrogen, C1-C10 alkyl, cycloalkyl or aryl;
or optionally, R2 and R3, together with the nitrogen atom to which they are attached form a cyclic moiety that may include an additional heteroatom selected from O, S and N;
each Bx is, independently, a heterocyclic base moiety or a blocked heterocyclic base moiety; and
each R1 is, independently, H, a blocked hydroxyl group, a sugar substituent group or a blocked sugar substituent group; comprising the steps of:
(a) providing a 5xe2x80x2-O-protected compound of the formula: 
wherein:
T1 is a hydroxyl protecting group; and
T2 is a covalent attachment to a support media, or a support media bound nucleoside, nucleotide, oligonucleoside or oligonucleotide;
(b) treating said 5xe2x80x2-O-protected compound with a deprotecting reagent for a time and under conditions effective to form a 5xe2x80x2-O-deprotected compound;
(c) coupling said 5xe2x80x2-O-deprotected compound with an activated phosphorus composition of the formula: 
wherein:
T3 is a hydroxyl protecting group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
R4 is N(L1)L2;
each L1 and L2 is, independently, C1-6 straight or branched alkyl, or a C5-7 cyclic aliphatic ring system;
or L1 and L2 are joined together to form a 4- to 13-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S; and
R5 is X1;
or R4 and R5 together with the phosphorus atom to which R4 and R5 are attached form a chiral auxiliary;
for a time and under conditions effective to form an extended compound having the formula: 
(d) treating said extended compound with dimethylthiuram disulfide in a solvent thereby forming a sulfurized compound having the formula: 
(e) treating said sulfurized compound with a capping reagent for a time and under conditions effective to form said oligomeric compound.
In one embodiment the dimethylthiuram disulfide is from about 0.02M to about 0.2M in said solvent. In a preferred embodiment the dimethylthiuram disulfide is from about 0.1M to about 0.2M in said solvent.
The present invention also provides methods of preparing oligomeric compounds having at least one moiety having one of the formulas: 
wherein:
X2 is O or S;
X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, C1-C10 straight or branched chain alkyl, CH3(CH2)nnxe2x80x94Oxe2x80x94, R2R3Nxe2x80x94 or a group remaining from coupling a chiral auxiliary;
nn is from 0 to 10;
Pg is CH3, xe2x80x94CH2CH2CN, xe2x80x94C(CH3)(CH3)xe2x80x94CCl3, xe2x80x94CH2xe2x80x94CCl3, xe2x80x94CH2CHxe2x95x90CH2, CH2CH2SiCH3, 2-yl-ethyl phenylsulfonate, xcex4-cyanobutenyl, cyano p-xylyl, diphenylsilylethyl, 4-nitro-2-yl-ethylbenzene, 2-yl-ethyl-methyl sulfonate, methyl-N-trifluoroacetyl ethyl, acetoxy phenoxy ethyl, or a blocking group;
each R2 and R3 is, independently, hydrogen, C1-C10 alkyl, cycloalkyl or aryl;
or optionally, R2 and R3, together with the nitrogen atom to which they are attached form a cyclic moiety that may include an additional heteroatom selected from O, S and N;
each Bx is, independently, a heterocyclic base moiety or a blocked heterocyclic base moiety; and
each R1 is, independently, H, a blocked hydroxyl group, a sugar substituent group or a blocked sugar substituent group;
comprising the steps of:
(a) providing a 5xe2x80x2-O-protected compound having one of the formulas: 
wherein:
T1 is a hydroxyl protecting group; and
T2 is a covalent attachment to a support media, or a support media bound nucleoside, nucleotide, oligonucleoside or oligonucleotide;
(b) treating said 5xe2x80x2-O-protected compound with a deprotecting reagent for a time and under conditions effective to form a 5xe2x80x2-O-deprotected compound;
(c) coupling said 5xe2x80x2-O-deprotected compound with an activated phosphorus composition of the formula: 
wherein:
T3 is a hydroxyl protecting group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide; R4 is N(L1)L2;
each L1 and L2 is, independently, C1-6 straight or branched alkyl, or a C5-7 cyclic aliphatic ring system;
or L1 and L2 are joined together to form a 4- to 13-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S; and
R5 is X1;
or R4 and R5 together with the phosphorus atom to which R4 and R5 are attached form a chiral auxiliary;
for a time and under conditions effective to form an extended compound having one of the formulas: 
and
(d) treating said extended compound with a mixture comprising an oxidizing reagent and a capping reagent for a time and under conditions effective to form said oligomeric compound.
The present invention is directed to methods for synthesizing oligonucleotides and analogs thereof having at least one moiety of one of the formulas: 
wherein:
X2 is O or S;
X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, C1-C10 straight or branched chain alkyl, CH3(CH2)nnxe2x80x94Oxe2x80x94, R2R3Nxe2x80x94 or a group remaining from coupling a chiral auxiliary;
nn is from 0 to 10;
Pg is CH3, xe2x80x94CH2CH2CN, xe2x80x94C(CH3)(CH3)-CCl3, xe2x80x94CH2xe2x80x94CCl3, xe2x80x94CH2CHxe2x95x90CH2 CH2CH2SiCH3, 2-yl-ethyl phenylsulfonate, xcex4-cyanobutenyl, cyano p-xylyl, diphenylsilylethyl, 4-nitro-2-yl-ethylbenzene, 2-yl-ethyl-methyl sulfonate, methyl-N-trifluoroacetyl ethyl, acetoxy phenoxy ethyl, or a blocking group;
each R2 and R3 is, independently, hydrogen, C1-C10 alkyl, cycloalkyl or aryl;
or optionally, R2 and R3, together with the nitrogen atom to which they are attached form a cyclic moiety that may include an additional heteroatom selected from O, S and N;
each Bx is, independently, a heterocyclic base moiety or a blocked heterocyclic base moiety; and
each R1 is, independently, H, a blocked hydroxyl group, a sugar substituent group, or a blocked substituent group;
The present methods can further include deblocking, deprotecting and cleaving the resulting oligomeric compound. The most common deblocked forms of X1 include xe2x80x94OH, xe2x80x94SH, xe2x80x94N(R2) (R3), alkyl and alkoxy groups. Purification can be performed at various stages, but is routinely performed with the terminal protecting group attached such as a trityl on purification. including protected or deprotected.
The most widely used method for the large scale synthesis of oligomeric compounds uses phosphoramidite chemistry on a support media. In general the method requires 4 separate and distinct steps per cycle: detritylation, coupling, oxidation and capping. Each step requires automated synthesis equipment time and significant quantities of reagents. In one aspect of the present invention, a method is disclosed that employs a mixture comprising an oxidizing reagent and a capping reagent to simultaneously effect oxidation of internucleoside linkages and capping of unreacted hydroxyl groups. This combined oxidation and capping step is amenable to otherwise standard synthetic methods for the synthesis of oligomeric compounds.
In general, a synthon bound to a support media, e.g. a nucleoside or nucleosidic oligomer, is extended by addition of a further synthon using standard chemistries to form a phosphite or other PIII intermediate linkage. Treatment of this PIII intermediate linkage in a single step with a mixture containing an oxidizing reagent and a capping reagent will give an extended compound having the desired Pv oxidized linkage with unreacted hydroxyl groups capped. Advantages of the present methods can include a faster synthesis time and a reduction in cost due in part to the deletion of one of the reagent consuming steps and associated wash and rinse cycles. A further advantage can be gained by selecting an inexpensive oxidizing reagent or one that is easily prepared from inexpensive reagents.
Preferred mixtures of oxidizing and capping reagents include those that are stable and include components that are mutually soluble with each other. Oxidizing reagents amenable to the present invention should be soluble in the solution comprising the oxidizing reagent at concentrations of 0.02M, or greater, preferred about 0.1M or more, more preferred from 0.1 to 0.2M. A preferred mixture is an oxidizing reagent dissolved in cap A (20% acetic anhydride in acetonitrile) mixed with an equal volume of cap B (N-methylimidazole-pyridine-acetonitrile, 2:3:5, v/v/v). Oxidizing reagents that are soluble and stable with an equal volume mixture of cap A and cap B are preferred within the scope of the present invention.
Oxidizing reagents that are effective to transfer an oxygen atom (thereby converting a PIII linkage to a PV linkage) include without limitation m-chloroperbenzoic acid; iodobenzene diacetate, tetra-n-butylammonium periodate; tert-butyl hydroperoxide; di-tert-butyl hydroperoxide; cumene hydroperoxide; hydrogen peroxide; bis-trimethylsilyl peroxide; and catalytic amounts of trimethylsilyl triflate; dinitrogen tetroxide and molecular oxygen in the presence of 2,2xe2x80x2-azobis(2-methylpropionitrile) under thermal or photo-chemical conditions; and (1S)-(+)-(10-camphorsulfonyl)-oxaziridine; iodine/tetrahydrofuran/water/pyridine; hydrogen peroxide/water; tert-butyl hydroperoxide; and a peracid like m-chloroperbenzoic acid (see review article Beaucage et al., Current Protocols in Nucleic Acid Chemistry, 2000, 3.3.1-3.3.20). In the case of oxidation to a sulfur species (sulfurization), the reaction is generally performed under anhydrous conditions with an exclusion of air, e.g. oxygen. In the case of oxidation the reaction can be performed under aqueous conditions.
Oxidizing reagents that transfer a sulfur atom (sulfurizing reagents) are used to form phosphorothioate or other sulfurized internucleoside linkages such as, for example, phosphorodithioate internucleoside linkages. Sulfurizing reagents amenable to the present invention include those that are partially or completely soluble in a selected capping reagent or reagents. In addition the sulfurizing reagent should be compatible e.g. stable and non-reactive with the capping reagents. Preferred sulfurizing reagents are commercially available in bulk for considerably less cost than most traditional sulfurizing agents that are currently in use. Alternatively, a sulfurizing reagent is selected because of its ease of synthesis from inexpensive bulk reagents.
One important criteria for a preferred sulfurizing reagent is its ability incorporate sulfur and exclude incorporation of oxygen. Analysis of an oxidized oligomer, using 31P NMR, will give the percentages of sulfurized and oxygenized internucleoside linkages.
Preferred sulfurized linkages include those that are prepared by methods known in the art to give chirally enhanced or chirally pure sulfurized linkages for those linkages that are not achiral. Preferred sulfurized linkages that are prepared by the present methods include:
phosphorothioate (xe2x80x94Oxe2x80x94P(S)(O)xe2x80x94Oxe2x80x94);
phosphorodithioate (xe2x80x94Oxe2x80x94P(S)(S)xe2x80x94Oxe2x80x94);
phosphorthioamidate (xe2x80x94Oxe2x80x94P(S)(NJ)xe2x80x94Oxe2x80x94);
phosphonothioate (xe2x80x94Oxe2x80x94P(J)(S)xe2x80x94Oxe2x80x94);
boranothiophosphate (xe2x80x94Oxe2x80x94P(S) (BJ3)xe2x80x94Jxe2x80x94);
wherein xe2x80x9cJxe2x80x9d denotes a substituent group which is commonly hydrogen or an alkyl group, but which can be a more complicated group that varies from one type of linkage to another but is well known to the art skilled.
Representative United States patents that teach the preparation of the above phosphorus atom containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,166,387; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; and 5,697,248, certain of which are commonly owned by the assignee of this application, and each of which is herein incorporated by reference.
Positional modifications, also known in the art, involve the linking of nucleosides in a non-naturally occurring motif. As used herein the term xe2x80x9cpositional modificationxe2x80x9d is meant to include without limitation 2xe2x80x2,5xe2x80x2-internucleoside linkages. Combining modifications e.g. using modified chemistries and positional modifications of selected internucleoside linkages is also amenable to the present invention where for example a 2xe2x80x2,5xe2x80x2-phosphoramidate internucleoside linkage is employed. The 2xe2x80x2-5xe2x80x2-linkage has been used at the termini of oligomeric compounds to enhance the nuclease resistance (as described in U.S. Application Serial No. 09/435,806, filed Nov. 8, 1999).
A representative list of substituent groups amenable to the present invention include C1-C20 alkyl, C2-C20 alkenyl, C2-C20 alkynyl, C5-C20 aryl, O-alkyl, O-alkenyl, O-alkynyl, O-alkylamino, (O-alkyl-N(H)alkyl ), O-alkylaminodialkyl (O-alkyl-N-(alkyl)2), O-alkylalkoxy (O-alkyl-O-alkyl), O-alkyl-(N-imidazole), S-alkenyl, S-alkynyl, NH-alkyl, NH-alkenyl, NH-alkynyl, N-dialkyl, O-aryl, S-aryl, NH-aryl, O-aralkyl, S-aralkyl, NH-aralkyl, N-phthalimido, halogen (particularly fluoro), keto, carboxyl, nitro, nitroso, nitrile, trifluoromethyl, trifluoromethoxy, imidazole, azido, hydrazino, hydroxylamino, isocyanato, sulfoxide, sulfone, sulfide, disulfide, silyl, heterocycle, carbocycle, polyamine, polyamide, polyalkylene glycol, and polyethers of the formula (O-alkyl)m, where m is 1 to about 10. Preferred among these polyethers are linear and cyclic polyethylene glycols (PEGs), and (PEG)-containing groups, such as crown ethers and those which are disclosed by Ouchi et al. (Drug Design and Discovery 1992, 9, 93), Ravasio et al. (J. Org. Chem. 1991, 56, 4329) and Delgardo et. al. (Critical Reviews in Therapeutic Drug Carrier Systems 1992, 9, 249), each of which is herein incorporated by reference in its entirety. Further sugar modifications are disclosed in Cook, P.D., Anti-Cancer Drug Design, 1991, 6, 585-607. Fluoro, O-alkyl, O-alkylamino, O-alkyl imidazole, O-alkylaminoalkyl, and alkyl amino substitution is described in U.S. patent application Ser. No. 08/398,901, filed Mar. 6, 1995, entitled Oligomeric Compounds having Pyrimidine Nucleotide(s) with 2xe2x80x2 and 5xe2x80x2 Substitutions, hereby incorporated by reference in its entirety.
Additional substituent groups amenable to the present invention include xe2x80x94SR and xe2x80x94NR2 groups, wherein each R is, independently, hydrogen, a protecting group or substituted or unsubstituted alkyl, alkenyl, or alkynyl. 2xe2x80x2-SR nucleosides are disclosed in U.S. Pat. No. 5,670,633, issued Sep. 23, 1997, hereby incorporated by reference in its entirety. The incorporation of 2xe2x80x2-SR monomer synthons are disclosed by Hamm et al., J. Org. Chem., 1997, 62, 3415-3420. 2xe2x80x2-NR2 nucleosides are disclosed by Goettingen, M., J. Org. Chem., 1996, 61, 6273-6281; and Polushin et al., Tetrahedron Lett., 1996, 37, 3227-3230.
Further substituent groups have one of formula I or II: 
wherein:
Z0 is O, S or NH;
J is a single bond, O or C(xe2x95x90O);
E is C1-C10 alkyl, N(R1) (R2), N(R1) (R5), Nxe2x95x90C(R1) (R2), Nxe2x95x90C(R1) (R5) or has one of formula III or IV; 
each R6, R7, R8, R9 and R10 is, independently, hydrogen, C(O)R11, substituted or unsubstituted C2-C10 alkyl, substituted or unsubstituted C2-C10 alkenyl, substituted or unsubstituted C2-C10 alkynyl, alkylsulfonyl, arylsulfonyl, a chemical functional group or a conjugate group, wherein the substituent groups are selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, alkyl, aryl, alkenyl and alkynyl;
or optionally, R7 and R8, together form a phthalimido moiety with the nitrogen atom to which they are attached;
or optionally, R9 and R10, together form a phthalimido moiety with the nitrogen atom to which they are attached;
each R11 is, independently, substituted or unsubstituted C1-C10 alkyl, trifluoromethyl, cyanoethyloxy, methoxy, ethoxy, t-butoxy, allyloxy, 9-fluorenylmethoxy, 2-(trimethylsilyl)-ethoxy, 2,2,2-trichloroethoxy, benzyloxy, butyryl, isobutyryl, phenyl or aryl;
R5 is T-L,
T is a bond or a linking moiety;
L is a chemical functional group, a conjugate group or a solid support material;
each R1 and R2 is, independently, H, a nitrogen protecting group, substituted or unsubstituted C1-C10 alkyl, substituted or unsubstituted C1-C10 alkenyl, substituted or unsubstituted C2-C10 alkynyl, wherein said substitution is OR3, SR3, NH3+, N(R3) (R4), guanidino or acyl where said acyl is an acid amide or an ester;
or R1 and R2, together, are a nitrogen protecting group or are joined in a ring structure that optionally includes an additional heteroatom selected from N and O;
or R1, T and L, together, are a chemical functional group;
each R3 and R4 is, independently, H, C1-C10 alkyl, a nitrogen protecting group, or R3 and R4, together, are a nitrogen protecting group;
or R3 and R4 are joined in a ring structure that optionally includes an additional heteroatom selected from N and O;
Z4 is OX, SX, or N(X)2;
each X is, independently, H, C1-C8 alkyl, C1-C8 haloalkyl, C(xe2x95x90NH)N(H)R5, C(xe2x95x90O)N(H)R5 or OC(xe2x95x90O)N(H)R5;
R5 is H or C1-C8 alkyl;
Z1, Z2 and Z3 comprise a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2 hetero atoms wherein said hetero atoms are selected from oxygen, nitrogen and sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic;
Z5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(R1) (R2) OR1, halo, SR1 or CN;
each q1 is, independently, an integer from 1 to 10;
each q2 is, independently, 0 or 1;
q3 is 0 or an integer from 1 to 10;
q4 is an integer from 1 to 10;
q5 is from 0, 1 or 2; and
provided that when q3 is 0, q4 is greater than 1.
Representative substituent groups of Formula I are disclosed in U.S. patent application Ser. No. 09/130,973, filed Aug. 7, 1998, entitled xe2x80x9cCapped 2xe2x80x2-Oxyethoxy Oligonucleotides,xe2x80x9d hereby incorporated by reference in its entirety.
Representative cyclic substituent groups of Formula II are disclosed in U.S. patent application Ser. No. 09/123,108, filed Jul. 27, 1998, entitled xe2x80x9cRNA Targeted 2xe2x80x2-Modified Oligonucleotides that are Conformationally Preorganized,xe2x80x9d hereby incorporated by reference in its entirety.
Particularly preferred substituent groups include O [(CH2)nO]mCH3, O(CH2)nOCH3, O(CH2)nNH2, O(CH2)nCH3, O(CH2)nONH2, O(CH2)nON[(CH2)nCH3)]2 (where n and m are from 1 to about 10), C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3 OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino and substituted silyl. Another particularly preferred modification includes 2xe2x80x2-methoxyethoxy (2xe2x80x2-Oxe2x80x94CH2CH2OCH3 or 2xe2x80x2-MOE, Martin et al., Helv. Chim. Acta, 1995, 78, 486). A further preferred substituent group is 2xe2x80x2-dimethylamino-oxyethoxy, i.e., a O(CH2)2ON(CH3)2 group, also known as 2xe2x80x2-DMAOE. Representative aminooxy substituent groups are described in co-owned U.S. patent application Ser. No. 09/344,260, filed Jun. 25, 1999, entitled xe2x80x9cAminooxy-Functionalized Oligomersxe2x80x9d; and U.S. patent application Ser. No. 09/370,541, filed Aug. 9, 1999, entitled Aminooxy-Functionalized Oligomers and Methods for Making Same; hereby incorporated by reference in their entirety.
Other preferred modifications include 2xe2x80x2-methoxy (2xe2x80x2-Oxe2x80x94CH3), 2xe2x80x2-aminopropoxy (2xe2x80x2-OCH2CH2CH2N2) and 2xe2x80x2-fluoro (2xe2x80x2-F). Similar modifications may also be made at other positions on nucleosides and oligomers, particularly the 3xe2x80x2 position of the sugar on the 3xe2x80x2 terminal nucleoside or at a 3xe2x80x2-position of a nucleoside that has a linkage from the 2xe2x80x2-position such as a 2xe2x80x2-5xe2x80x2 linked oligomer and at the 5xe2x80x2-position at a 5xe2x80x2-terminus. Oligomers may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugars structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,0531 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned, and each of which is herein incorporated by reference, and commonly owned U.S. patent application Ser. No. 08/468,037, filed on Jun. 5, 1995, also herein incorporated by reference.
Representative guanidino substituent groups that are shown in formula III and IV are disclosed in co-owned U.S. patent application 09/349,040, entitled xe2x80x9cFunctionalized Oligomersxe2x80x9d, filed Jul. 7, 1999, hereby incorporated by reference in its entirety.
Representative acetamido substituent groups are disclosed in U.S. patent application Ser. No. 09/378,568, entitled xe2x80x9c2xe2x80x2-O-Acetamido Modified Monomers and Oligomersxe2x80x9d, filed Aug. 19, 1999, hereby incorporated by reference in its entirety.
Representative dimethylaminoethyloxyethyl substituent groups are disclosed in International Patent Application PCT/US99/17895, entitled xe2x80x9c2xe2x80x2-O-Dimethylaminoethyloxyethyl-Modified Oligonucleotidesxe2x80x9d, filed Aug. 6, 1999, hereby incorporated by reference in its entirety.
The use of mixed modifications in the terminal regions of an oligonucleotide to impart nuclease resistance is also within the scope of the present invention. For example an oligomeric compound of the invention can have enhanced nuclease resistance resulting from one or more modified internucleoside linkages at the 5xe2x80x2 end and one or more substituent groups at the 3xe2x80x2 end. Another type of a mixed modification includes having a modified internucleoside linkage and a substituent group at the same end of a selected oligomeric compound. Other examples include substituent groups or modified linkages used in conjunction with a non-standard linkage such as a 2xe2x80x2, 5xe2x80x2-internucleoside linkage.
Oligomeric compounds according to the present invention preferably comprise from about 5 to about 50 nucleosides. It is more preferred that such compounds comprise from about 8 to about 30 nucleosides, with 15 to 25 nucleosides being particularly preferred.
In general, the term xe2x80x9cheteroxe2x80x9d denotes an atom other than carbon, preferably but not exclusively N, O, or S. Accordingly, the term xe2x80x9cheterocyclic ringxe2x80x9d denotes an alkyl ring system having one or more heteroatoms (i.e., non-carbon atoms). Heterocyclic ring structures of the present invention can be fully saturated, partially saturated, unsaturated or with a polycyclic heterocyclic ring each of the rings may be in any of the available states of saturation. Heterocyclic ring structures of the present invention also include heteroaryl, which includes fused systems including systems where one or more of the fused rings contain no heteroatoms. Heterocycles, including nitrogen heterocycles, according to the present invention include, but are not limited to, imidazole, pyrrole, pyrazole, indole, 1H-indazole, xcex1-carboline, carbazole, phenothiazine, phenoxazine, tetrazole, triazole, pyrrolidine, piperidine, piperazine and morpholine groups. A more preferred group of nitrogen heterocycles includes imidazole, pyrrole, indole, and carbazole groups.
A heterocyclic base moiety (often referred to in the art simply as a xe2x80x9cbasexe2x80x9d or a xe2x80x9cnucleobasexe2x80x9d) amenable to the present invention includes both naturally and non-naturally occurring nucleobases. The heterocyclic base moiety further may be protected wherein one or more functionalities of the base bears a protecting group. As used herein, xe2x80x9cunmodifiedxe2x80x9d or xe2x80x9cnaturalxe2x80x9d nucleobases include the purine bases adenine and guanine, and the pyrimidine bases thymine, cytosine and uracil. Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in the Concise Encyclopedia of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley and Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993.
Certain nucleobases are particularly useful for increasing the binding affinity of oligomeric compounds. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2xc2x0 C. (Id., pages 276-278) and are presently preferred base substitutions, even more particularly when combined with 2xe2x80x2-methoxyethyl sugar modifications.
Representative United States patents that teach the preparation of modified nucleobases include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; and 5,681,941, certain of which are commonly owned, and each of which is herein incorporated by reference, and commonly owned U.S. patent application Ser. No. 08/762,488, filed on Dec. 10, 1996, also herein incorporated by reference.
The attachment of conjugate groups to oligomers is well documented in the prior art. The present methods include preparation of oligomeric compounds that include conjugate groups covalently bound to functional groups such as primary or secondary hydroxyl groups. Conjugate groups of the invention include intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers. Typical conjugates groups include cholesterols, phospholipids, biotin, phenazine, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups that enhance the pharmacodynamic properties, in the context of this invention, include groups that improve oligomer uptake, enhance oligomer resistance to degradation, and/or strengthen sequence-specific hybridization with RNA. Groups that enhance the pharmacokinetic properties, in the context of this invention, include groups that improve oligomer uptake, distribution, metabolism or excretion. Representative conjugate groups are disclosed in International Patent Application PCT/US92/09196, filed Oct. 23, 1992, U.S. Pat. No. 5,578,718, issued Jul. 1, 1997, and U.S. Pat. No. 5,218,105.
Each of the foregoing is commonly assigned with this application. The entire disclosure of each is incorporated herein by reference.
Preferred conjugate groups amenable to the present invention include lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 111; Kabanov et al., FEBS Lett., 1990, 259, 327; Svinarchuk et al., Biochimie, 1993, 75, 49), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium-1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651; Shea et al., Nucl. Acids Res., 1990, 18, 3777), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides and Nucleotides, 1995, 14, 969), adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923).
Other groups that can be attached to oligomeric compounds to modify antisense properties include RNA cleaving complexes, pyrenes, metal chelators, porphyrins, alkylators, hybrid intercalator/ligands and photo-crosslinking agents. RNA cleavers include o-phenanthroline/Cu complexes and Ru(bipyridine)32+ complexes. The Ru(bpy)32+ complexes are believed to interact with nucleic acids and cleave nucleic acids photochemically. Metal chelators include EDTA, DTPA, and o-phenanthroline. Alkylators include compounds such as iodoacetamide. Porphyrins include porphine, its substituted forms, and metal complexes. Pyrenes include pyrene and other pyrene-based carboxylic acids that could be conjugated using the similar protocols.
As used herein, xe2x80x9cpolyaminexe2x80x9d refers to a moiety containing a plurality of amine or substituted amine functionalities. Polyamines according to the present invention have at least two amine functionalities. xe2x80x9cPolypeptidexe2x80x9d refers to a polymer comprising a plurality of amino acids linked by peptide linkages, and includes dipeptides and tripeptides. The amino acids may be naturally-occurring or non-naturally-occurring amino acids. Polypeptides according to the present invention comprise at least two amino acids.
The methods of the present invention can employ activated phosphorus compositions in coupling reactions. As used herein, the term activated phosphorus composition includes activated phosphorus containing monomers or oligomers that are reactive with a hydroxyl group of another monomeric or oligomeric compound to form a phosphorus-containing internucleotide linkage. Such activated phosphorus groups contain activated phosphorus atoms in PIII valence state. Such activated phosphorus atoms are known in the art and include, but are not limited to, phosphoramidite and chiral auxiliary moieties. A preferred synthesis utilizes phosphoramidites as activated phosphorus groups. Additional activated phosphites are disclosed in Tetrahedron Report Number 309 (Beaucage and Iyer, Tetrahedron, 1992, 48, 2223-2311).
Representative activated phosphorus containing monomers or oligomers include those having the formula: 
wherein each Bx is, independently, a heterocyclic base moiety or blocked heterocyclic base moiety; and
each R1 is, independently, H, a blocked hydroxyl group, a sugar substituent group, or a blocked substituent group;
T3 is an hydroxyl protecting group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
R4 is N(L1)L2; each L1 and L2 is, independently, C1-6 straight or branched alkyl, or a C5-7 cyclic aliphatic ring system;
or L1 and L2 are joined together to form a 4- to 13-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S; and
R5 is X1;
X1 is Pgxe2x80x94Oxe2x80x94, Pgxe2x80x94Sxe2x80x94, C1-C10 straight or branched chain alkyl, CH3(CH2)nnxe2x80x94Oxe2x80x94, R2R3Nxe2x80x94 or a group remaining from coupling a chiral auxiliary;
nn is from 0 to 10;
Pg is CH3, xe2x80x94CH2CH2CN, xe2x80x94C(CH3) (CH3)xe2x80x94CCl3, xe2x80x94CH2xe2x80x94CCl3, xe2x80x94CH2CHxe2x95x90CH2 CH2CH2SiCH3, 2-yl-ethyl phenylsulfonate, xcex4-cyanobutenyl, cyano p-xylyl, diphenylsilylethyl, 4-nitro-2-yl-ethylbenzene, 2-yl-ethyl-methyl sulfonate, methyl-N-trifluoroacetyl ethyl, acetoxy phenoxy ethyl, or a blocking group;
each R2 and R3 is, independently, hydrogen, C1-C10 alkyl, cycloalkyl or aryl;
or optionally, R2 and R3, together with the nitrogen atom to which they are attached form a cyclic moiety that may include an additional heteroatom selected from O, S and N; or
R4 and R5 together with the phosphorus atom to which R4 and R5 are attached form a chiral auxiliary.
Groups that are attached to the phosphorus atom of internucleotide linkages before and after oxidation (R4 and R5) can include nitrogen containing cyclic moieties such as morpholine. Such oxidized internucleoside linkages include a phosphoromorpholidothioate linkage (Wilk et al., Nucleosides and nucleotides, 1991, 10, 319-322). Further cyclic moieties amenable to the present invention include mono-, bi- or tricyclic ring moieties which may be substituted with groups such as oxo, acyl, alkoxy, alkoxycarbonyl, alkyl, alkenyl, alkynyl, amino, amido, azido, aryl, heteroaryl, carboxylic acid, cyano, guanidino, halo, haloalkyl, haloalkoxy, hydrazino, ODMT, alkylsulfonyl, nitro, sulfide, sulfone, sulfonamide, thiol and thioalkoxy. A preferred bicyclic ring structure that includes nitrogen is phthalimido.
Some representative examples of R4 and R5 groups which are known to the art skilled and are amenable to the present invention are shown below:
Functional groups including substituent groups discussed above which may be located on heterocyclic base and sugar moieties are routinely blocked with protecting (blocking groups) during synthesis and subsequently deblocked. In general, a blocking group renders a chemical functionality of a molecule inert to specific reaction conditions and can later be removed from such functionality in a molecule without substantially damaging the remainder of the molecule. See, Green and Wuts, Protective Groups in Organic Synthesis, 2d edition, John Wiley and Sons, New York, 1991. For example, amino groups can be blocked with nitrogen protecting groups such as phthalimido, 9-fluorenylmethoxycarbonyl (FMOC), triphenylmethylsulfenyl, t-BOC or benzyl groups. Carboxyl groups can be protected as acetyl groups. Representative hydroxyl protecting groups are described by Beaucage et al., Tetrahedron 1992, 48, 2223. Preferred hydroxyl protecting groups are acid-labile groups, such as the trityl, monomethoxytrityl, dimethoxytrityl, trimethoxytrityl, 9-phenylxanthin-9-yl (Pixyl) and 9-(p-methoxyphenyl)xanthin-9-yl (MOX). Chemical functional groups can also be xe2x80x9cblockedxe2x80x9d by including them in a precursor form. Thus an azido group can be considered a xe2x80x9cblockedxe2x80x9d form of an amine as the azido group is easily converted to the amine. Further representative protecting groups utilized in oligonucleotide synthesis are discussed in Agrawal et al., Protocols for Oligonucleotide Conjugates, Eds., Humana Press, New Jersey, 1994, Vol. 26, pp. 1-72.
Standard oligonucleotide synthesis using phosphite (PIII) chemistry involves treatment of the growing oligomer with a deprotecting reagent to create a free hydroxyl position that is available for a further coupling reaction. Hydroxyl protecting groups are preferably removed using a weak acid. Dependant on the choice of protecting group the deprotecting reagent can be acidic, basic, neutral or fluoride mediated. A representative list of deprotecting reagents amenable to the present methods includes without limitation protic acids used for removing acid labile protecting groups such as dichloro- and trichloroacetic acids, Lewis acids such as BF3-etherate, zinc bromide, AlCl1, TiCl4, (Et)AlCl, (I-Bu)2AlCl and other reagents such as ceric ammonium nitrate, 1,1,1,3,3,3-hexafluoro-2-propanol, and diethyloxomalonate. A preferred deprotecting reagent that is used routinely for example for the removal of various trityl protecting groups is 2-5% dichloroacetic acid in either dichloromethane or dichloroethane.
The use of blocking groups is common practice to protect or block reactive or functional groups that are typically located on or linked to nucleobases, internucleotide linkages and sugars. Generally, blocking groups are removed using conditions that are stronger than those encountered during the iterative elongation steps in oligomer synthesis. This allows for deprotection of hydroxyl groups and coupling without effecting blocked positions. As used herein, the term xe2x80x9cblocking groupxe2x80x9d describes a group that is stable to the conditions that are used to deprotect groups such as hydroxyl groups during the iterative elongation steps of oligomeric compound synthesis. Blocking groups are generally removed after the desired length has been synthesized. Standard phosphoramidite chemistry frequently uses acid labile protecting groups on hydroxyls that are used for coupling steps and strong base labile blocking groups to block other reactive positions not used in coupling steps. Many examples of protecting and blocking groups are collectively described in for example Green and Wuts ibid. Preferred blocking groups are removed by treatment with base. Some representative base labile protecting groups include without limitation, Fmoc (E. Atherton and R. C. Sheppard in The Peptides, S. Udenfriend, J. Meienhofer, Eds., Academic Press, Orlando, 1987, volume 9, p.1), and various substituted sulfonylethyl carbamates exemplified by the Nsc group (Samukov et al., Tetrahedron Lett, 1994, 35:7821; Verhart and Tesser, Rec. Trav. Chim. Pays-Bas, 1987, 107:621).
After synthesis the resulting oligomeric compound generally is cleaved from the solid support to obtain the free oligomer. The step of deprotecting the blocked 5xe2x80x2-O-hydroxyl is usually performed separately as this is generally accomplished using an acidic deblocking reagent. This step is routinely performed after deprotection, cleavage and purification has been performed to enhance the purification process by keeping the terminal hydroxyl blocked. The deprotection and cleavage steps can be separated into separate steps or combined into a single step depending on the particular protecting groups, solid support linking groups and the choice of reagent or reagents used. In a preferred embodiment the simultaneous deprotection and cleavage of the final oligomeric compound following synthesis is accomplished in one step using a solution of ammonium hydroxide (NH4OH (30%) for 15 hours at 60xc2x0 C., filtered, rinsed with ethanol/water (1/1, v/v), the combined solutions are evaporated to dryness under vacuum).
The purification of oligomeric compounds is generally by reversed phase high performance liquid chromatography (RP-HPLC) performed on a Waters Nova-Pak C18 column (3.9xc3x97300 mm) using a Waters HPLC system (600E System Controller, 996 Photodiode Array Detector, 717 Autosampler). For analysis an acetonitrile (A)/0.1M triethylammonium acetate gradient is used: 5% to 35% A from 0 to 10 min, then 35% to 40% A from 10 to 20 min, then 40% to 95% A from 20 to 25 min, flow rate=10 mL/min/50% A from 8 to 9 min, 9 to 26 min at 50%, flow rate=1.0 mL/min, tR(DMT-off) 10-11 min, tR(DMT-on) 14-16 min. The DMT-on fractions are collected and are evaporated in vacuum, redissolved in water and the DMT group removed as described below.
Removal of the final hydroxyl protecting group from the 5xe2x80x2hydroxyl group is generally performed by treatment with an acidic solution such as acetic acid. The oligomeric compound is treated with the acidic solution for about 30 minutes at room temperature. The mixture is further treated with sodium acetate and cold ethanol followed by vortexing and cooling with dry ice. The precipitate is centrifuged, separated, washed and dried to give the final deprotected product.
The term xe2x80x9cnucleosidexe2x80x9d as used in connection with this invention refers to a monomeric unit made up of a heterocyclic base moiety joined to a sugar moiety or sugar mimetic through a glycosyl linkage. The term xe2x80x9cnucleotidexe2x80x9d refers to a nucleoside having a phosphate group on its 3xe2x80x2 or 5xe2x80x2 sugar hydroxyl group.
In the context of this invention, the terms xe2x80x9coligomerxe2x80x9d and xe2x80x9coligomeric compoundxe2x80x9d refer to a plurality of naturally-occurring or non-naturally-occurring nucleosides joined together in a specific sequence. The terms xe2x80x9coligomerxe2x80x9d and xe2x80x9coligomeric compoundxe2x80x9d include oligonucleotides, oligonucleotide analogs, oligonucleosides and chimeric oligomeric compounds where there are more than one type of internucleoside linkages dividing the oligomeric compound into regions. Whereas the term xe2x80x9coligonucleotidexe2x80x9d has a well defined meaning in the art, the term xe2x80x9coligomeric compoundxe2x80x9d or xe2x80x9coligomerxe2x80x9d is intended to be broader, inclusive of oligomers having all manner of modifications known in the art. Gapped or chimeric compounds are disclosed in for example, U.S. Pat. No. 5,623,065, issued Apr. 22, 1997, the contents of which are incorporated herein by reference.
As used herein, the term xe2x80x9coligonucleosidexe2x80x9d includes oligomers or polymers containing two or more nucleoside subunits having a non-phosphodiester linking moiety. Oligonucleosides according to the invention have a ribofuranose moiety attached to a nucleobase through a glycosyl bond.
Gapmer technology has been developed to incorporate modifications at the ends (xe2x80x9cwingsxe2x80x9d) of oligomeric compounds, leaving a phosphorothioate gap in the middle for RNase H activation (Cook, P. D., Anti-Cancer Drug Des., 1991, 6, 585-607; Monia et al., J. Biol. Chem., 1993, 268, 14514-14522). In a recent report, the activities of a series of uniformly 2xe2x80x2-O modified 20 mer RNase H-independent oligonucleotides that were antisense to the 5xe2x80x2-cap region of human ICAM-1 transcript in HUVEC cells, were compared to the parent 2xe2x80x2-deoxy phosphorothioate oligonucleotide (Baker et al., J. Bio. Chem., 1997, 272, 11994-12000). The 2xe2x80x2-MOE/Pxe2x95x90O oligomer demonstrated the greatest activity with an IC50 of 2.1 nM (Tm=87.1xc2x0 C.), while the parent Pxe2x95x90S oligonucleotide analog had an IC50 of 6.5 nM (Tm=79.2xc2x0 C.). Correlation of activity with binding affinity is not always observed as the 2xe2x80x2-F/Pxe2x95x90S (Tm=87.9xc2x0 C.) was less active than the 2xe2x80x2-MOE/Pxe2x95x90S (Tm=79.2xc2x0 C.) by four fold. The RNase H competent 2xe2x80x2-deoxy Pxe2x95x90S parent oligonucleotide exhibited an IC50=41 nM.
As used herein the term xe2x80x9cchiral auxiliaryxe2x80x9d is meant to include groups that function to provide chirality to internucleoside phosphorus linkages during synthesis. Chiral auxiliaries amenable to the present invention include those that form a PIII intermediate capable of being oxidized. Chiral auxiliaries will give either Sp or Rp chirality for the respective internucleoside linkage in the final oligomeric compound. Accordingly, chiral auxiliaries are allowed to remain on the growing chain, and are removed at the end of the iterative synthetic regime. Removal of chiral auxiliaries can be conveniently accomplished in a single treatment after the completion of the iterative synthesis. Chiral auxiliaries and methods of their incorporation using standard protocols are disclosed in commonly owned U.S. patent application Ser. No. 09/438,989, filed on Nov. 12, 1999, incorporated herein by reference. Further chiral auxiliaries have been previously reported for use in the preparation of oligomeric phosphorothioates (see Iyer et al., Tetrahedron letters, 1998, 39, 2491-2494 and Wilk et al., J. Am. Chem. Soc., 2000, 122, 2149-2156). Representative chiral auxiliaries include, without limitation those having the following formulas: 
As used herein, the term xe2x80x9calkylxe2x80x9d includes, but is not limited to, straight chain, branched chain and alicyclic hydrocarbon groups. Alkyl groups of the present invention may be substituted. Representative alkyl substituents are disclosed in U.S. Pat. No. 5,212,295, at column 12, lines 41-50, hereby incorporated by reference in its entirety. Substituent groups include, but are not limited to, alkyl, alkenyl, alkynyl, aryl, hydroxyl, alkoxy, alcohol, benzyl, phenyl, nitro, thiol, thioalkoxy, thioalkyl, trifluoromethyl, halo, nitrile, trifluoromethoxy and azido. As used herein, the term xe2x80x9clower alkylxe2x80x9d is intended to mean an alkyl group having 10 or fewer carbons.
Alkenyl groups according to the invention are to straight chain, branch chain, and cyclic hydrocarbon groups containing at least one carbon-carbon double bond, and alkynyl groups are to straight chain, branch chain, and cyclic hydrocarbon groups containing at least one carbon-carbon triply bond. Alkenyl and alkynyl groups of the present invention can be substituted.
Aryl groups are substituted and unsubstituted aromatic cyclic moieties including but not limited to phenyl, naphthyl, anthracyl, phenanthryl, pyrenyl, and xylyl groups. Alkaryl groups are those in which an aryl moiety links an alkyl moiety to a core structure, and aralkyl groups are those in which an alkyl moiety links an aryl moiety to a core structure.
As used herein, the term xe2x80x9caralkylxe2x80x9d denotes alkyl groups which bear aryl groups, for example, benzyl groups. The term xe2x80x9calkarylxe2x80x9d denotes aryl groups which bear alkyl groups, for example, methylphenyl groups. As used herein, the term xe2x80x9carylxe2x80x9d denotes aromatic cyclic groups including, but not limited to, phenyl, naphthyl, anthracyl, phenanthryl and pyrenyl. Preferred aryl and aralkyl groups include, but are not limited to, phenyl, benzyl, xylyl, naphthyl, toluyl, pyrenyl, anthracyl, azulyl, phenethyl, cinnamyl, benzhydryl, and mesityl. Typical substituents for substitution include, but are not limited to, hydroxyl, alkoxy, alcohol, benzyl, phenyl, nitro, thiol, thioalkoxy, halogen, or alkyl, aryl, alkenyl, or alkynyl groups.
As used herein, the term xe2x80x9calkanoylxe2x80x9d has its accustomed meaning as a group of formula xe2x80x94C(xe2x95x90O)-alkyl. A preferred alkanoyl group is the acetyl group.
In one aspect of the present invention oligomeric compounds are prepared using support bound methodologies wherein the oxidation and capping steps are combined into a single step. A first modified or unmodified nucleoside is attached to a support media preferably via a linkage to the 3xe2x80x2-position. The nucleoside could alternatively be attached to a support media through the 2xe2x80x2-position as when preparing positionally modified internucleoside linkages. Alternatively, the support media with the desired nucleoside attached can be purchased from a number of commercial sources. In a traditional synthesis this nucleoside will ultimately become the nucleoside at the 3xe2x80x2-end of the final oligomeric compound. The support media with the nucleoside attached is placed in a reaction vessel such as a glass reactor. One of the hydroxyl groups (preferably the 5xe2x80x2-hydroxyl group) is deprotected and treated with a second nucleoside having a group reactive with the hydroxyl group such as an activated phosphorus group or a chiral auxiliary. This coupling step is preferably performed in the presence of an activating agent such as DBU or 1-H-tetrazole. The linkage thus formed is treated with a mixture containing reagents for oxidizing and capping. A preferred mixture for incorporating a sulfur atom is (0.3M) dimethylthiuram disulfide in cap A (20% acetic anhydride in acetonitrile) mixed with and equal volume of cap B (20% N-methylimidazole, 30% pyridine and 50% aetonitrile, by volume). The cycle is optionally repeated to add additional nucleosides until the desired oligomeric compound is completed.
As used herein, the term xe2x80x9csulfurizing reagentxe2x80x9d includes without limitation, dimethylthiuram disulfide (Cummings et al., Ind. Eng. Chem., 1928, 20, 1173); 1,2,4-dithiazolidine-3,5-dione (DTSNH, see Xu et al., Nucleic Acids Research, 1996, 24, 1602-1607); 3-methyl-1,2,4-dithiazolin-5-one (MEDITH, see Zang et al., Tetrahedron Lett., 1999, 40, 2095-20980); phenylacetyl disulfide (PADS, see Kamer et al., Tetrahedron Lett., 1989, 30, 6757-6760; Cheruvallath et al., Organic Process Research and Development, 2000, 4, 199-204); tetraethylthiuram disulfide (TETD, see Vu et al., Tetrahedron Lett., 1991, 32, 3005-3008); 3H-1,2-benzodithiol-3-one-1,1-dioxide (Beaucage reagent, see e.g. Iyer, R. P., et.al., J. Chem. Soc., 1990, 112, 1253-1254, and Iyer, R. P., et.al., J. Org. Chem., 1990, 55, 4693-4699); tetraethylthiuram disulfide (see e.g., Vu, H., Hirschbein, B. L., Tetrahedron Lett., 1991, 32, 3005-3008); dibenzoyl tetrasulfide (see e.g., Rao, M. V., et.al., Tetrahedron Lett., 1992, 33, 4839-4842); benzyltriethylammonium tetrathiomolybdate (BTTM, see e.g., Rao, M. V., et.al., Tetrahedron Lett., 1994, 35, 6741-6744); di(phenylacetyl)disulfide (see e.g., Kamer, P. C. J., Tetrahedron Lett., 1989, 30, 6757-6760); Bis(O,O-diisopropoxy phosphinothioyl)disulfides (see Stec et al., Tetrahedron Lett., 1993, 34, 5317-5320); 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH, see Xu et al., Nucleic Acids Research, 1996 24, 1602-1607, and Nucleic Acids Research, 1996 24, 3643-3644); Bis(p-chlorobenzenesulfonyl)disulfide (see Nucleic Acids Research, 1995 23, 4029-4033); bis(ethoxythiocarbonyl)-tetrasulfide (see Zang et al., Tetrahedron Lett., 1998, 39, 2467-2470); bis(p-toluenesulfonyl)disulfide (Efimov et al., Nucleic Acids Res., 1995, 23, 4029-4033); 3-amino-1,2,4-dithiazole-5-thione (see Org. Process Res. Dev., 2000, 4, 194-198); ethylthiuram disulfide CAS #3082-38-0; 5,6-dihydro-3H-imidazo[2,1-C]-1,2,4-dithiazole-3-thione CAS #33813-20-6; 4-methyl-5-(methylimino)-1,2,4-dithiazolidine-3-thione CAS #20042-85-7; sulfur, sulfur in combination with ligands like triaryl, trialkyl, triaralkyl, or trialkaryl phosphines. The foregoing references are hereby incorporated by reference in their entirety.
A preferred list of sulfurizing reagents includes: 3-amino-1,2,4-dithiazole-5-thione; 3-ethoxy-1,2,4-dithiazoline-5-one; 1,2,4-dithiazolidine-3,5-dione; 3-methyl-1,2,4-dithiazolin-5-one; and dimethylthiuram disulfide.
A representative list of capping reagents useful in the methods of the present invention include without limitation, acetic anhydride, t-butylphenoxyacetic anhydride, phosphite monoesters, and selected acid chlorides preferably delivered concurrently with a nucleophilic catalyst (e.g. a strong base) such as for example N-methylimidazole or triethylamine. Generally capping reagents comprise a mixture of Cap A and Cap B. Representative mixtures include without limitation:
Cap A: acetic anhydride in acetonitrile or tetrahydrofuran;
chloroacetic anhydride in acetonitrile or tetrahydrofuran;
Cap B: N-methylimidazole and pyridine in acetonitrile or tetrahydrofuran;
4-dimethylaminopyridine (DMAP) and pyridine in acetonitrile or tetrahydrofuran;
2,6-lutidine and N-methylimidazole in acetonitrile or tetrahydrofuran.
A more detailed description capping reagents is discussed in U.S. Pat. No. 4,816,571, issued Mar. 28, 1989 which is incorporated herein by reference. A preferred capping reagent is acetic anhydride routinely used as a mixture of cap A and cap B.
During the coupling step one compound having an active phosphate is coupled to a second compound having a free hydroxyl group. An activating agent is not believed to be essential for this step but one is generally used to increase the reaction efficiency. A list of activators and references for each can be found in Eleueri et al., Organic Process Research and Development, 2000, 4, 182-189. Preferred activators include without limitation: 1H-tetrazole, 5-(2-nitrophenyl)-1H-tetrazole, 5-(p-nitrophenyl)-1H-tetrazole, 5-trifluoromethyl-1H-tetrazole, 5-ethylthio-1H-tetrazole, 5-benzyltio-1H-tetrazole, 2,4,5-tribromoimidazole, 2-nitroimidazole, 4,5-dichloroimidazole, 2-bromo-4,5-dicyanoimidazole, 4,5-dicyanoimidazole, N-methylimidazole hydrochloride, 1-hydroxybenzotriazole, 5-chlorobenzotriazole, chlorotrimethylsilane, benzimidazolium triflate, imidazolium triflate, pyridinium hydrochloride/imidazole, pyridinium tetrafluoroborate, pyridinium chloride, pyridinium bromide, pyridinium 4-methylbenzinesulfonate, N-methylimidazolium trifluroborate, N-methylanilinium trichloroacetate, N-methylanilinium trifluoroacetate, 1H-tetrazole/DMAP, 1H-tetrazole/N-methylimidazole, and N-methylimidazolium trifluoromethanesulfonate (see see review article Beaucage et al., Current Protocols in Nucleic Acid Chemistry, 2000, 3.3.1-3.3.20).
The current method of choice for the preparation of oligomeric compounds uses support media. Support media is used to attach a first nucleoside or larger nucleosidic synthon which is then iteratively elongated to give a final oligomeric compound. Support media can be selected to be insoluble or have variable solubility in different solvents to allow the growing oligomer to be kept out of or in solution as desired. Traditional solid supports are insoluble and are routinely placed in a reaction vessel while reagents and solvents react and or wash the growing chain until cleavage frees the final oligomer. More recent approaches have introduced soluble supports including soluble polymer supports to allow precipitating and dissolving the bound oligomer at desired points in the synthesis (Gravert et al., Chem. Rev., 1997, 97, 489-510). Representative support media that are amenable to the methods of the present invention include without limitation: controlled pore glass (CPG); oxalyl-controlled pore glass (see, e.g., Alul, et al., Nucleic Acids Research 1991, 19, 1527); TENTAGEL Support, (see, e.g., Wright, et al., Tetrahedron Letters 1993, 34, 3373); or POROS, a copolymer of polystyrene/divinylbenzene available from Perceptive Biosystems. The use of a soluble support media, poly(ethylene glycol), with molecular weights between 5 and 20 kDa, for large-scale synthesis of phosphorothioate oligonucleotides is described in, Bonora et al., Organic Process Research and Development, 2000, 4, 225-231.
It was previously reported (Cummings A. D. et al. Ind. Eng. Chem., 1928, 20, 1173) that dimethylthiuram disulfide was not a stable compound and decomposes slowly on standing. The dimethylthiuram disulfide, after standing for 1 month, failed to show a melting point of 102xc2x0 C. The decomposition products were identified as hydrogen sulfide, elemental sulfur and methyl isothiocyanate. The lack of long shelf life for dimethylthiuram disulfide has been attributed to the dithiocabamate derivative of methylamine, which is a primary amine. The present invention provides a new and improved procedure for the synthesis of dimethylthiuram disulfide (see Example 7) which utilizes an acid wash at the end of the synthesis. The primary amine is protonated which stabilizes the dithiocarbamate structure from degradation. A further improvement was realized by oxidizing the intermediate with hydrogen peroxide as opposed to iodine. This led to the preparation of white crystalline product instead of the yellow unstable product previously reported. Dimethylthiuram disulfide made by this protocol is very stable even after six months of storage at room temperature.
Oligomeric compounds prepared by the methods of the present invention can be used in diagnostics, therapeutics and as research reagents and kits. They can also be used in pharmaceutical compositions by including a suitable pharmaceutically acceptable diluent or carrier. They can further be used for treating organisms having a disease characterized by the undesired production of a protein. For this purpose, the organism is contacted with an oligomer having a sequence that is capable of specifically hybridizing with a strand of nucleic acid encoding the undesirable protein. Treatments of this type can be practiced on a variety of organisms ranging from unicellular prokaryotic and eukaryotic organisms to multicellular eukaryotic organisms. Any organism that utilizes DNA-RNA transcription or RNA-protein translation as a fundamental part of its hereditary, metabolic or cellular control is susceptible to therapeutic and/or prophylactic treatment in accordance with the invention. Seemingly diverse organisms such as bacteria, yeast, protozoa, algae, all plants and all higher animal forms, including warm-blooded animals, can be treated. Further, each cell of multicellular eukaryotes can be treated, as they include both DNA-RNA transcription and RNA-protein translation as integral parts of their cellular activity. Furthermore, many of the organelles (e.g., mitochondria and chloroplasts) of eukaryotic cells also include transcription and translation mechanisms. Thus, single cells, cellular populations or organelles can also be included within the definition of organisms that can be treated with therapeutic or diagnostic oligomeric compounds of the invention.
Those skilled in the art will appreciate that numerous changes and modifications may be made to the preferred embodiments of the invention and that such changes and modifications may be made without departing from the spirit of the invention. It is, therefore, intended that the appended claims cover all such equivalent variations as fall within the true spirit and scope of the invention.